In deponent-verb/popgen.stats: Popgen summary statistics calculator

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(popgen.stats)

The popgen_stats package is a popgen pipeline that produces genetic simulations via the coalescent simulator program discoal. The package requires discoal to be working on the user's terminal.

Let's simulate some genomes using the discoal_sim function.

  #input parameters
  mu=1e-8
  recomb_rate=1e-9
  Ne=1000000
  nSites=1e5
  samplesize=20
  s=0.1
  fix_generation=1

  #path to discoal program
  discoal_path="~/work/programs/discoal/discoal"

  sim<-discoal_sim(mu,recomb_rate,Ne,nSites,samplesize,s,discoal_path,fix_generation)